clintval vartovcf issues

clintval / vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.

MIT License

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Use a peekable iterator to set the sample name?

#84 clintval opened 4 months ago
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chore: update dependencies and linting

#83 clintval closed 4 months ago
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Confirm our new VCF keys are what we want to go with and publish comparison documentation

#82 clintval opened 2 years ago
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Use proglog in stead of homebrew progress counter

#81 clintval closed 4 months ago
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Ensure the quality score is being calculated correctly

#80 clintval closed 4 months ago
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feat: do not emit duplicate variant calls and tidy up all INFO keys

#79 clintval closed 2 years ago
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feat: skip meaningless records in VarDict output

#78 clintval closed 2 years ago
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chore: tidy up places in the code with to-dos

#77 clintval closed 2 years ago
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We support `var2vcf_valid.pl` so we should also support `var2vcf_paired.pl`

#76 clintval opened 2 years ago
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feat: add gVCF support and correctly set the GT field

#75 clintval closed 2 years ago
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Output the right GT fields using the same logic as `vartovcf_valid.pl`

#74 clintval closed 2 years ago
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feat: do not remove duplicates from stdout, downstream tools need to

#73 clintval closed 2 years ago
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Drop support for duplicate VCF records (when a user supplies overlapping BEDs)

#72 clintval closed 2 years ago
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Progress logger always formats it's emissions to come from it's own class

#71 clintval closed 2 years ago
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Implement a record peek to parameterize the header based on the input data

#70 clintval closed 2 years ago
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Build a variant struct to communicate what to write on each loop

#69 clintval closed 2 years ago
1
Disallow duplicate variant call records in VCF output

#68 clintval closed 3 years ago
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Ensure we only emit each variant record once

#67 clintval closed 3 years ago
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Ensure strand bias odds ratio is serialized correctly

#66 clintval closed 3 years ago
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Move README.md image to .github folder

#65 clintval closed 3 years ago
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Generalize the name of the integration on-disk test data

#64 clintval closed 3 years ago
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Use a FromStr helper for PairBias deserialization

#63 clintval closed 3 years ago
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Fix an off by one error in TumorOnlyVariant length

#62 clintval closed 3 years ago
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Fix a small double negative in documentation

#61 clintval closed 3 years ago
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Further test new code paths, increase coverage

#60 clintval closed 3 years ago
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Ensure we handle the gVCF cases gracefully, according to spec.

#59 clintval closed 2 years ago
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Set all INFO and FILTER fields to alphabetical ordering

#58 clintval closed 3 years ago
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Parse SV metadata into a struct and send to output VCF

#57 clintval closed 3 years ago
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Implement the modes we intend to support on the CLI

#56 clintval closed 3 years ago
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Try the pure Rust noodles library!

#55 clintval closed 3 years ago
1
Ensure VCFs are completely free of warnings from popular validators

#54 clintval closed 3 years ago
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Add all FORMAT keys from upstream

#53 clintval closed 3 years ago
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Add all FORMAT fields

#52 clintval closed 3 years ago
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Update the benchmarks on a slightly larger file

#51 clintval closed 3 years ago
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Implement a progress logger

#50 clintval closed 3 years ago
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Add the reference genome filepath to the VCF header

#49 clintval closed 3 years ago
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Return an exception if the sample is unexpected

#48 clintval closed 3 years ago
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Learn how to use custom errors, test them too

#47 clintval closed 3 years ago
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Added CLI integration tests for streaming STDIN/STDOUT scenarios

#46 clintval closed 3 years ago
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If someone wants to write streaming bcf, how?

#45 clintval closed 3 years ago
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Sort all keys in each section alphabetically

#44 clintval closed 3 years ago
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Add an integration test for streaming IO

#43 clintval closed 3 years ago
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Add a unit test for when the input sample is wrong

#42 clintval closed 3 years ago
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Implement a ProgressLogger like in htsjdk/fgbio?

#41 clintval closed 3 years ago
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Add a custom type for ref/alt strand bias, serde too

#40 clintval closed 3 years ago
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Handle IO for file/STDIN/STDOUT elegantly

#39 clintval closed 3 years ago
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Add a Windows build and test to CI harness

#38 clintval closed 3 years ago
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Add a helper method for getting a FASTA FAI from FASTA

#37 clintval closed 3 years ago
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Have builds run all tests for Linux and MacOS

#36 clintval closed 3 years ago
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Add a single successful test of the CLI

#35 clintval closed 3 years ago
0